Monitoring immunoglobulin heavy chain evolution in B-cell acute lymphoblastic leukemia

Abstract

The invention is directed to methods of monitoring B-cell lymphoid proliferative disorders, such as B-cell acute lymphoblastic leukemias, by measuring the presence, absence and/or levels of correlating, or index, clonotypes and related clonotypes that have evolved therefrom, for example, as part of the disease condition. In one aspect, such methods are implemented by generating sequencing-based clonotype profiles and determining frequencies of correlating, or index, clonotypes present, including new clonotypes that have evolved therefrom, particularly, in the case of B-cell ALL, by VH substitution. The invention also includes use of such monitoring information to modify treatment status of a patient.

What is claimed is: 
     
       1. A method of determining that a clonotype is evolved by V H  substitution from one or more patient-specific clonotypes correlated with a B-cell acute lymphoblastic leukemia (ALL), the method comprising:
 (a) amplifying nucleic acid molecules from B-cells in a sample from a B-cell ALL patient, the nucleic acid molecules comprising or derived from recombined DNA sequences from immunoglobulin genes, thereby generating amplified nucleic acid molecules; 
 (b) sequencing the amplified nucleic acid molecules to form a clonotype profile; and 
 (c) determining from the clonotype profile that a clonotype evolved by V H  substitution from one or more patient-specific clonotypes correlated with the B-cell ALL, wherein the clonotype is considered evolved from a patient-specific clonotype correlated with the B-cell ALL if at least six consecutive nucleotides extending in a V H  direction from a J-NDN boundary are identical in the evolved clonotype and the clonotype correlated with the B-cell ALL. 
 
     
     
       2. The method of  claim 1 , further comprising repeating steps (a) through (c) on nucleic acid molecules from a successive sample from the patient to determine from the clonotype profile formed from the amplified nucleic acid molecules from the successive sample that a clonotype evolved by V H  substitution from one or more patient-specific clonotypes correlated with the B-cell ALL. 
     
     
       3. The method of  claim 1 , wherein the nucleic acid molecules comprise at least a portion of a VDJ region. 
     
     
       4. The method of  claim 1 , wherein the clonotype profile includes every clonotype present among the amplified nucleic acid molecules at a frequency of 0.001 percent or greater with a probability of ninety-nine percent. 
     
     
       5. The method of  claim 1 , wherein the clonotype profile includes at least 10 4  clonotypes. 
     
     
       6. The method of  claim 1 , wherein the sample is a sample of bone marrow or a sample of peripheral blood. 
     
     
       7. The method of  claim 1 , wherein the V H  substitution is a V H  replacement. 
     
     
       8. The method of  claim 1 , further comprising determining from the clonotype profile the presence, absence and/or level of the one or more patient-specific clonotypes and the evolved clonotype. 
     
     
       9. The method of  claim 8 , further comprising a step of modifying a treatment of the B-cell ALL of the patient based on the presence, absence and/or level of the one or more patient-specific clonotypes and the evolved clonotype. 
     
     
       10. The method of  claim 2 , further comprising determining from the clonotype profile the presence, absence and/or level of the one or more patient-specific clonotypes and the evolved clonotype in the sample and the successive sample and comparing the levels of the one or more patient-specific clonotypes and the evolved clonotype in the sample and the successive sample. 
     
     
       11. The method of  claim 10 , wherein (a) the B-cell ALL is a childhood ALL, (b) the level of the one or more patient-specific clonotypes and the evolved clonotype increases in the successive sample, and (c) the step of modifying a treatment comprises administering an anti-ALL agent different from an anti-ALL agent administered in an induction therapy. 
     
     
       12. The method of  claim 10 , wherein (a) the B-cell ALL is a childhood ALL, (b) the level of the one or more patient-specific clonotypes and the evolved clonotype increases in the successive sample, and (c) the step of modifying a treatment comprises performing a bone marrow transplant on the patient. 
     
     
       13. The method of  claim 1 , wherein the step of determining comprises comparing the at least six consecutive nucleotides extending V H  direction from a J-NDN boundary in a clonotype from the clonotype profile with the one or more patient-specific clonotypes and/or previously recorded clonotypes clonally evolved by V H  substitution from the one or more patient-specific clonotypes. 
     
     
       14. The method of  claim 13 , wherein a clonotype from the clonotype profile is considered evolved from one or more patient-specific clonotypes correlated with the B-cell ALL based on identity of at least six consecutive nucleotides extending in a V H  direction from a J-NDN boundary and likelihoods of occurrence of J segments, J deletions, NDN segments, V segments, or V deletions based on databases of clonotype sequences from populations of individuals. 
     
     
       15. The method of  claim 14 , wherein a clonotype from the clonotype profile is considered evolved from one or more patient-specific clonotypes correlated with the B-cell ALL based on likelihoods of occurrence in the B-cell ALL of D segments, positions of D segments in NDN segments, J-side deletions of D segments, or V-side deletions of D segments. 
     
     
       16. The method of  claim 1 , wherein the determination of a clonotype from the clonotype profile as evolved from one or more patient-specific clonotypes correlated with the B-cell ALL is made by using a naive Bayesian classifier model. 
     
     
       17. The method of  claim 1 , wherein the evolved clonotype is a previously unrecorded clonotype.